VMD-L Mailing List

From: Dan Wright (dtwright_at_uiuc.edu)
Date: Tue May 08 2007 - 16:58:43 CDT

You may need to have these commands in a file called .bash_profile
rather then .bashrc. bash will source one or the other of these files
depending on how it is called; to solve the problem so you don't have to
worry about it, run "ln -s .bashrc .bash_profile" to make a symbolic
link .bash_profile -> .bashrc.

Dan

Ralph Jimenez wrote:
> John,
> As you suggested, I created the .bashrc file in my home directory, then
> started VMD, then ran the puts "$env(VMDMSMSUSEFILE)" command, but VMD
> doesn't see the environment variable. It says:
> can't read "env(VMDMSMSUSEFILE)": no such variable
>
> Thanks,
> Ralph
>
>
> John Stone wrote:
>> Ralph,
>> I don't have a mac in front of me just now, but yes, just try
>> creating a .bashrc file in your home directory consisting of those
>> two commands. You can determine whether VMD is seeing the environment
>> variable by running this command in the VMD text console:
>> puts "$env(VMDMSMSUSEFILE)"
>>
>>> From there, try starting VMD and using MSMS once the variable is
>> set correctly.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>>
>> On Tue, May 08, 2007 at 11:12:33AM -0600, Ralph Jimenez wrote:
>>> John,
>>> Thanks. However, I opened a terminal window and looked in my home
>>> directory (ls -l .*) and did not find a .bashrc or .profile file. My
>>> login shell is set to bash. Where should the .bashrc file be located,
>>> and if I don't find one, should I just create it, with those two
>>> commands you mentioned?
>>> Ralph
>>>
>>>
>>>
>>> John Stone wrote:
>>>> Hi,
>>>> If your login shell on OSX is set to bash, then you'd add these
>>>> commands
>>>> to your .bashrc or .profile file:
>>>> VMDMSMSUSEFILE=1
>>>> export VMDMSMSUSEFILE
>>>>
>>>> If you're using csh, then you'd add these to .cshrc:
>>>> setenv VMDMSMSUSEFILE 1
>>>>
>>>> Cheers,
>>>> John Stone
>>>> vmd_at_ks.uiuc.edu
>>>>
>>>> On Mon, May 07, 2007 at 08:37:38PM -0600, Ralph Jimenez wrote:
>>>>> Dear VMDers:
>>>>>
>>>>> I downloaded MSMS from TSRI's web site, but it doesn't work,
>>>>> probably because my environment variables aren't set. I get the
>>>>> "Could not connect to MSMS server..." error message.
>>>>>
>>>>> I need help with two things, which are alluded to in several places
>>>>> in the VMD docs and mailing list, but I need more explicit
>>>>> instructions:
>>>>>
>>>>> 1. Could someone please tell me which commands need to be added to
>>>>> which file so that VMD finds msms?
>>>>>
>>>>> 2. The 1.8.6 release notes say "it is necessary to set the
>>>>> VMDMSMSUSEFILE environment variable to work around incompatible
>>>>> endianness..." So which command do I need to add to which file to
>>>>> do this part?
>>>>>
>>>>> Thanks for your time.
>>>>> Ralph
>>>>>
>>>>>
>>>>> --
>>>>> -----------------------------------------------
>>>>>
>>>>> Ralph Jimenez, Ph.D.
>>>>> JILA/NIST and Department of Chemistry & Biochemistry
>>>>> 440 UCB
>>>>> University of Colorado, Boulder
>>>>> Boulder, CO 80309-0440
>>>>>
>>>>> Tel: (303) 492-8439
>>>>> FAX: (303) 492-5235
>>>>>
>>>>> http://jilawww.colorado.edu/JimenezLab/
>>>
>>> --
>>> Ralph Jimenez, Ph.D.
>>> JILA/NIST and Department of Chemistry & Biochemistry
>>> 440 UCB
>>> University of Colorado, Boulder
>>> Boulder, CO 80309-0440
>>>
>>> Tel: (303) 492-8439
>>> FAX: (303) 492-5235
>>>
>>> http://jilawww.colorado.edu/JimenezLab/
>>
>
>